Detecting selection in population trees: The Lewontin and Krakauer test extended

Genetics

Volumn 186, Issue 1, 2010, Pages 241-262

  Bonhomme, Maxime ^a   Chevalet, Claude ^a   Servin, Bertrand ^a   Boitard, Simon ^a   Abdallah, Jihad ^a,b   Blott, Sarah ^c   SanCristobal, Magali ^a,b  

^a CEMAGREF   (France)

^b AN NAJAH NATIONAL UNIVERSITY   (Palestine)

^c ANIMAL HEALTH TRUST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREEDING; CHI SQUARE DISTRIBUTION; DEMOGRAPHY; GENE FREQUENCY; GENETIC DRIFT; GENETIC HETEROGENEITY; GENETIC SELECTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; SWINE;

ANIMALS; EVOLUTION, MOLECULAR; GENETIC DRIFT; GENETIC MARKERS; GENETICS, POPULATION; MODELS, GENETIC; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC; SWINE;

SUIDAE;

EID: 78751653688     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.117275     Document Type: Article

References (40)

1. BALDING, D., 2003 Likelihood-based inference for genetic correlation coefficients. Theor. Popul. Biol. 63(3): 221-230.
2. BARREIRO, L., G. LAVAL, H. QUACH, E. PATIN and L. QUINTANA-MURCI, 2008 Natural selection has driven population differentation in modern humans. Nat. Genet. 40(3): 340-345.
3. BEAUMONT, M., 2005 Adaptation and speciation: What can f-st tell us? Trends Ecol. Evol. 20(8): 435-440.
4. BEAUMONT, M., and D. BALDING, 2004 Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol. 13(4): 969-980.
5. BEAUMONT, M., and R. NICHOLS, 1996 Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Lond. Ser. B Biol. Sci. 263(1377): 1619-1626.
6. BEAUMONT, M., W. ZHANG and D. BALDING, 2002 Approximate Bayesian computation in population genetics. Genetics 162: 2025-2035.
7. BENJAMINI, Y., and Y. HOCHBERG, 1995 Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 57(1): 289-300.
8. BLOTT, S., L. ANDERSSON, M. GROENEN, M. SAN CRISTOBAL, C. CHEVALET et al., 2003 Characterisation of genetic variation in the pig breeds of China and Europe - the pigbiodiv2 project. Arch. Zootecnia 52(198): 207-217.
9. EVENO, E., C. COLLADA, M. GUEVARA, V. LÉGER, A. SOTO et al., 2008 Contrasting patterns of selection at pinus pinaster ait. drought stress candidate genes as revealed by genetic differentiation analyses. Mol. Biol. Evol. 25(2): 417-437.
10. EXCOFFIER, L., T. HOFER and M. FOLL, 2009 Detecting loci under selection in a hierarchically structured population. Heredity 103(4): 285-298.
11. FLINT, J., J. BOND, D. REES, A. BOYCE, J. ROBERTS-THOMSON et al., 1999 Minisatellite mutational processes reduce f(st) estimates. Hum. Genet. 105(6): 567-576.
12. FLORI, L., S. FRITZ, F. JAFFRÉZIC, M. BOUSSAHA, I. GUT et al., 2009 The genome response to artificial selection: a case study in dairy cattle. PLoS ONE 4(8): e6595.
13. FOLL, M., and O. GAGGIOTTI, 2008 A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180: 977-993.
14. GAUTIER, M., L. FLORI, A. RIEBLER, F. JAFFREZIC, D. LALOE et al., 2009 A whole genome Bayesian scan for adaptive genetic divergence in west African cattle. BMC Genomics 10: 550.
15. GUO, F., D. DEY and K. HOLSINGER, 2009 A Bayesian hierarchical model for analysis of snp diversity in multilocus, multipopulation samples. J. Am. Stat. Assoc. 104(485): 142-154.
16. HUDSON, R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18(2): 337-338.
17. LAVAL, G., M. SANCRISTOBAL and C. CHEVALET, 2002 Measuring genetic distances between breeds: use of some distances in various short term evolution models. Genet. Sel. Evol. 34(4): 481-507.
18. LEWONTIN, R. C., and J. KRAKAUER, 1973 Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.
19. LEWONTIN, R. C., and J. KRAKAUER, 1975 Testing heterogeneity of f-values. Genetics 80: 397-398.
20. LUIKART, G., P. ENGLAND, D. TALLMON, S. JORDAN and P. TABERLET, 2003 The power and promise of population genomics: from genotyping to genome typing. Nat. Rev. Genet. 4(12): 981-994.
21. MARJORAM, P., J. MOLITOR, V. PLAGNOL and S. TAVARÉ, 2003 Markov chain Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. USA 100(26): 15324-15328.
22. NEI, M., and A. CHAKRAVARTI, 1977 Drift variances of fst and gst statistics obtained from a finite number of isolated populations. Theor. Popul. Biol. 11(3): 307-325.
23. NEI, M., and T. MARUYAMA, 1975 Lewontin-Krakauer test for neutral genes-comment. Genetics 80: 395.
24. NEI, M., A. CHAKRAVARTI and Y. TATENO, 1977 Mean and variance of fst in a finite number of incompletely isolated populations. Theor. Popul. Biol. 11(3): 291-306.
25. NIELSEN, R., 2005 Molecular signatures of natural selection. Annu. Rev. Genet. 39: 197-218.
26. NORDBORG, M., 1997 Structured coalescent processes on different time scales. Genetics 146: 1501-1514.
27. REYNOLDS, J., B. WEIR and C. COCKERHAM, 1983 Estimation of the co-ancestry coefficient-basis for a short-term genetic-distance. Genetics 105: 767-779.
28. RIEBLER, A., L. HELD and W. STEPHAN, 2010 Bayesian variable selection for detecting adaptive genomic differences among populations. Genetics 178: 1817-1829.
29. ROBERTSON, A., 1975a Gene frequency distributions as a test of selective neutrality. Genetics 81: 775-785.
30. ROBERTSON, A., 1975b Lewontin-Krakauer test for neutral genes - comment. Genetics 80: 396.
31. SAITOU, N., and M. NEI, 1987 The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4(4): 406-425.
32. SANCRISTOBAL, M., C. CHEVALET, C. S. HALEY, R. JOOSTEN, A. P. RATTINK et al., 2006 Genetic diversity within and between European pig breeds using microsatellite markers. Anim. Genet. 37: 189-198.
33. STORZ, J., B. PAYSEUR and M. NACHMAN, 2004 Genome scans of dna variability in humans reveal evidence for selective sweeps outside of africa. Mol. Biol. Evol. 21(9): 1800-1811.
34. TANABE, K., and M. SAGAE, 1992 An exact Cholesky decomposition and the generalized inverse of the variance-covariance matrix of the multinomial distribution, with applications. J. R. Stat. Soc. Series B Stat. Methodol. 54: 211-219.
35. TSAKAS, S., and C. KRIMBAS, 1976 Testing the heterogeneity of f values: a suggestion and a correction. Genetics 84: 399-401.
36. VITALIS, R., K. DAWSON and P. BOURSOT, 2001 Interpretation of variation across marker loci as evidence of selection. Genetics 158: 1811-1823.
37. WAKELEY, J., 1999 Nonequilibrium migration in human history. Genetics 153: 1863-1871.
38. WAKELEY, J., 2001 The coalescent in an island model of population subdivision with variation among demes. Theor. Popul. Biol. 59(2): 133-144.
39. WAKELEY, J., and N. ALIACAR, 2001 Gene genealogies in a metapopulation. Genetics 159: 893-905.
40. WEIR, B., and W. HILL, 2002 Estimating f-statistics. Annu. Rev. Genet. 36: 721-750.